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Witherspoon VJ, Komlosh ME, Benjamini D, Özarslan E, Lavrik N, Basser PJ. Novel pore size-controlled, susceptibility matched, 3D-printed MRI phantoms. Magn Reson Med 2024; 91:2431-2442. [PMID: 38368618 DOI: 10.1002/mrm.30029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 12/14/2023] [Accepted: 01/02/2024] [Indexed: 02/20/2024]
Abstract
PURPOSE We report the design concept and fabrication of MRI phantoms, containing blocks of aligned microcapillaires that can be stacked into larger arrays to construct diameter distribution phantoms or fractured, to create a "powder-averaged" emulsion of randomly oriented blocks for vetting or calibrating advanced MRI methods, that is, diffusion tensor imaging, AxCaliber MRI, MAP-MRI, and multiple pulsed field gradient or double diffusion-encoded microstructure imaging methods. The goal was to create a susceptibility-matched microscopically anisotropic but macroscopically isotropic phantom with a ground truth diameter that could be used to vet advanced diffusion methods for diameter determination in fibrous tissues. METHODS Two-photon polymerization, a novel three-dimensional printing method is used to fabricate blocks of capillaries. Double diffusion encoding methods were employed and analyzed to estimate the expected MRI diameter. RESULTS Susceptibility-matched microcapillary blocks or modules that can be assembled into large-scale MRI phantoms have been fabricated and measured using advanced diffusion methods, resulting in microscopic anisotropy and random orientation. CONCLUSION This phantom can vet and calibrate various advanced MRI methods and multiple pulsed field gradient or diffusion-encoded microstructure imaging methods. We demonstrated that two double diffusion encoding methods underestimated the ground truth diameter.
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Affiliation(s)
- Velencia J Witherspoon
- Section on Quantitative Imaging and Tissue Sciences, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, USA
| | - Michal E Komlosh
- Section on Quantitative Imaging and Tissue Sciences, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, USA
- Center for Neuroscience and Regenerative Medicine, Uniformed Services of Health Sciences, Bethesda, Maryland, USA
| | - Dan Benjamini
- Section on Quantitative Imaging and Tissue Sciences, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, USA
- Multiscale Imaging and Integrative Biophysics Unit, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA
| | - Evren Özarslan
- Spin Nord AB, Linköping, Sweden
- Department of Biomedical Engineering, Linköping University, Linköping, Sweden
| | - Nickolay Lavrik
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Peter J Basser
- Section on Quantitative Imaging and Tissue Sciences, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, USA
- Center for Neuroscience and Regenerative Medicine, Uniformed Services of Health Sciences, Bethesda, Maryland, USA
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Ulloa P, Methot V, Wottschel V, Koch MA. Extra-axonal contribution to double diffusion encoding-based pore size estimates in the corticospinal tract. MAGMA (NEW YORK, N.Y.) 2023; 36:589-612. [PMID: 36745290 PMCID: PMC10468962 DOI: 10.1007/s10334-022-01058-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 12/14/2022] [Accepted: 12/19/2022] [Indexed: 02/07/2023]
Abstract
OBJECTIVE To study the origin of compartment size overestimation in double diffusion encoding MRI (DDE) in vivo experiments in the human corticospinal tract. Here, the extracellular space is hypothesized to be the origin of the DDE signal. By exploiting the DDE sensitivity to pore shape, it could be possible to identify the origin of the measured signal. The signal difference between parallel and perpendicular diffusion gradient orientation can indicate if a compartment is regular or eccentric in shape. As extracellular space can be considered an eccentric compartment, a positive difference would mean a high contribution to the compartment size estimates. MATERIALS AND METHODS Computer simulations using MISST and in vivo experiments in eight healthy volunteers were performed. DDE experiments using a double spin-echo preparation with eight perpendicular directions were measured in vivo. The difference between parallel and perpendicular gradient orientations was analyzed using a Wilcoxon signed-rank test and a Mann-Whitney U test. RESULTS Simulations and MR experiments showed a statistically significant difference between parallel and perpendicular diffusion gradient orientation signals ([Formula: see text]). CONCLUSION The results suggest that the DDE-based size estimate may be considerably influenced by the extra-axonal compartment. However, the experimental results are also consistent with purely intra-axonal contributions in combination with a large fiber orientation dispersion.
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Affiliation(s)
- Patricia Ulloa
- Institute of Medical Engineering, University of Luebeck, Ratzeburger Allee 160, 23562 Luebeck, Germany
| | - Vincent Methot
- Institute of Medical Engineering, University of Luebeck, Ratzeburger Allee 160, 23562 Luebeck, Germany
| | - Viktor Wottschel
- Department of Radiology and Nuclear Medicine, Amsterdam University Medical Centers, De Boelelaan 1117, 1081, Amsterdam, The Netherlands
| | - Martin A. Koch
- Institute of Medical Engineering, University of Luebeck, Ratzeburger Allee 160, 23562 Luebeck, Germany
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Measuring latency distribution of transcallosal fibers using transcranial magnetic stimulation. Brain Stimul 2020; 13:1453-1460. [PMID: 32791313 PMCID: PMC7417270 DOI: 10.1016/j.brs.2020.08.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 08/04/2020] [Accepted: 08/06/2020] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Neuroimaging technology is being developed to enable non-invasive mapping of the latency distribution of cortical projection pathways in white matter, and correlative clinical neurophysiological techniques would be valuable for mutual verification. Interhemispheric interaction through the corpus callosum can be measured with interhemispheric facilitation and inhibition using transcranial magnetic stimulation. OBJECTIVE To develop a method for determining the latency distribution of the transcallosal fibers with transcranial magnetic stimulation. METHODS We measured the precise time courses of interhemispheric facilitation and inhibition with a conditioning-test paired-pulse magnetic stimulation paradigm. The conditioning stimulus was applied to the right primary motor cortex and the test stimulus was applied to the left primary motor cortex. The interstimulus interval was set at 0.1 ms resolution. The proportions of transcallosal fibers with different conduction velocities were calculated by measuring the changes in magnitudes of interhemispheric facilitation and inhibition with interstimulus interval. RESULTS Both interhemispheric facilitation and inhibition increased with increment in interstimulus interval. The magnitude of interhemispheric facilitation was correlated with that of interhemispheric inhibition. The latency distribution of transcallosal fibers measured with interhemispheric facilitation was also correlated with that measured with interhemispheric inhibition. CONCLUSIONS The data can be interpreted as latency distribution of transcallosal fibers. Interhemispheric interaction measured with transcranial magnetic stimulation is a promising technique to determine the latency distribution of the transcallosal fibers. Similar techniques could be developed for other cortical pathways.
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Direct and specific assessment of axonal injury and spinal cord microenvironments using diffusion correlation imaging. Neuroimage 2020; 221:117195. [PMID: 32726643 PMCID: PMC7805019 DOI: 10.1016/j.neuroimage.2020.117195] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 07/17/2020] [Accepted: 07/21/2020] [Indexed: 12/17/2022] Open
Abstract
We describe a practical two-dimensional (2D) diffusion MRI framework to deliver specificity and improve sensitivity to axonal injury in the spinal cord. This approach provides intravoxel distributions of correlations of water mobilities in orthogonal directions, revealing sub-voxel diffusion components. Here we use it to investigate water diffusivities along axial and radial orientations within spinal cord specimens with confirmed, tract-specific axonal injury. First, we show using transmission electron microscopy and immunohistochemistry that tract-specific axonal beading occurs following Wallerian degeneration in the cortico-spinal tract as direct sequelae to closed head injury. We demonstrate that although some voxel-averaged diffusion tensor imaging (DTI) metrics are sensitive to this axonal injury, they are non-specific, i.e., they do not reveal an underlying biophysical mechanism of injury. Then we employ 2D diffusion correlation imaging (DCI) to improve discrimination of different water microenvironments by measuring and mapping the joint water mobility distributions perpendicular and parallel to the spinal cord axis. We determine six distinct diffusion spectral components that differ according to their microscopic anisotropy and mobility. We show that at the injury site a highly anisotropic diffusion component completely disappears and instead becomes more isotropic. Based on these findings, an injury-specific MR image of the spinal cord was generated, and a radiological-pathological correlation with histological silver staining % area was performed. The resulting strong and significant correlation (r = 0.70, p < 0.0001) indicates the high specificity with which DCI detects injury-induced tissue alterations. We predict that the ability to selectively image microstructural changes following axonal injury in the spinal cord can be useful in clinical and research applications by enabling specific detection and increased sensitivity to injury-induced microstructural alterations. These results also encourage us to translate DCI to higher spatial dimensions to enable assessment of traumatic axonal injury, and possibly other diseases and disorders in the brain.
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Ni Z, Vial F, Avram AV, Leodori G, Pajevic S, Basser PJ, Hallett M. Measuring conduction velocity distributions in peripheral nerves using neurophysiological techniques. Clin Neurophysiol 2020; 131:1581-1588. [PMID: 32417700 DOI: 10.1016/j.clinph.2020.04.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 04/12/2020] [Accepted: 04/13/2020] [Indexed: 12/16/2022]
Abstract
OBJECTIVE To determine how long it takes for neural impulses to travel along peripheral nerve fibers in living humans. METHODS A collision test was performed to measure the conduction velocity distribution of the ulnar nerve. Two stimuli at the distal and proximal sites were used to produce the collision. Compound muscle or nerve action potentials were recorded to perform the measurements on the motor or mixed nerve, respectively. Interstimulus interval was set at 1-5 ms. A quadri-pulse technique was used to measure the refractory period and calibrate the conduction time. RESULTS Compound muscle action potential produced by the proximal stimulation started to emerge at the interstimulus interval of about 1.5 ms and increased with the increment in interstimulus interval. Two groups of motor nerve fibers with different conduction velocities were identified. The mixed nerve showed a wider conduction velocity distribution with identification of more subgroups of nerve fibers than the motor nerve. CONCLUSIONS The conduction velocity distributions in high resolution on a peripheral motor and mixed nerve are different and this can be measured with the collision test. SIGNIFICANCE We provided ground truth data to verify the neuroimaging pipelines for the measurements of latency connectome in the peripheral nervous system.
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Affiliation(s)
- Zhen Ni
- Human Motor Control Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, United States
| | - Felipe Vial
- Human Motor Control Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, United States; Facultad de Medicina Clinica Alemana Universidad del Desarrollo, Santiago, Chile
| | - Alexandru V Avram
- National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, United States
| | | | - Sinisa Pajevic
- Mathematical and Statistical Computing Laboratory, Center for Information Technology, National Institutes of Health, United States
| | - Peter J Basser
- Section on Quantitative Imaging and Tissue Sciences, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, United States.
| | - Mark Hallett
- Human Motor Control Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, United States.
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Duchêne G, Abarca-Quinones J, Feza-Bingi N, Leclercq I, Duprez T, Peeters F. Double Diffusion Encoding for Probing Radiation-Induced Microstructural Changes in a Tumor Model: A Proof-of-Concept Study With Comparison to the Apparent Diffusion Coefficient and Histology. J Magn Reson Imaging 2020; 52:941-951. [PMID: 32147929 DOI: 10.1002/jmri.27119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 02/17/2020] [Accepted: 02/18/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Microstructure analyses are gaining interest in cancer MRI as an alternative to the conventional apparent diffusion coefficient (ADC), of which the determinants remain unclear. PURPOSE To assess the sensitivity of parameters calculated from a double diffusion encoding (DDE) sequence to changes in a tumor's microstructure early after radiotherapy and to compare them with ADC and histology. STUDY TYPE Cohort study on experimental tumors. ANIMAL MODEL Sixteen WAG/Rij rats grafted with one rhabdomyosarcoma fragment in each thigh. Thirty-one were imaged at days 1 and 4, of which 17 tumors received a 20 Gy radiation dose after the first imagery. FIELD STRENGTH/SEQUENCE 3T. Diffusion-weighted imaging, DDE with flow compensated, and noncompensated measurements. ASSESSMENTS 1) To compare, after irradiation, DDE-derived parameters (intracellular fraction, cell size, and cell density) to their histological counterparts (fraction of stained area, minimal Feret diameter, and nuclei count, respectively). 2) To compare percentage changes in DDE-derived parameters and ADC. 3) To evaluate the evolution of DDE-derived parameters describing perfusion. STATISTICAL TESTS Wilcoxon rank sum test. RESULTS 1) Intracellular fraction, cell size, and cell density were respectively lower (-24%, P < 0.001), higher (+7.5%, P < 0.001) and lower (-38%, P < 0.001) in treated tumors as compared to controls. Fraction of stained area, minimal Feret diameter, and nuclei count were respectively lower (-20%, P < 0.001), higher (+28%, P < 0.001), and lower (-34%, P < 0.001) in treated tumors. 2) The magnitude of ADC's percentage change due to irradiation (16.4%) was superior to the one of cell size (8.4%, P < 0.01) but inferior to those of intracellular fraction (35.5%, P < 0.001) and cell density (42%, P < 0.001). 3) After treatment, the magnitude of the vascular fraction's decrease was higher than the increase of flow velocity (33.3%, vs. 13.3%, P < 0.001). DATA CONCLUSION The DDE sequence allows quantitatively monitoring the effects of radiotherapy on a tumor's microstructure, whereas ADC only reveals global changes. EVIDENCE LEVEL 2. TECHNICAL EFFICACY Stage 4. J. Magn. Reson. Imaging 2020;52:941-951.
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Affiliation(s)
- Gaëtan Duchêne
- Department of medical imaging, Institut de Recherche Expérimentale et Clinique, Université Catholique de Louvain, Brussels, Belgium
| | - Jorge Abarca-Quinones
- Department of medical imaging, Institut de Recherche Expérimentale et Clinique, Université Catholique de Louvain, Brussels, Belgium.,MRI unit, Department of medical imaging, Cliniques Universitaires Saint-Luc, Brussels, Belgium
| | - Natacha Feza-Bingi
- Department of medical imaging, Institut de Recherche Expérimentale et Clinique, Université Catholique de Louvain, Brussels, Belgium.,Laboratory of Hepato-gastroenterology, Institut de Recherche Expérimentale et Clinique, Université catholique de Louvain, Brussels, Belgium
| | - Isabelle Leclercq
- Department of medical imaging, Institut de Recherche Expérimentale et Clinique, Université Catholique de Louvain, Brussels, Belgium.,MRI unit, Department of medical imaging, Cliniques Universitaires Saint-Luc, Brussels, Belgium.,Laboratory of Hepato-gastroenterology, Institut de Recherche Expérimentale et Clinique, Université catholique de Louvain, Brussels, Belgium
| | - Thierry Duprez
- Department of medical imaging, Institut de Recherche Expérimentale et Clinique, Université Catholique de Louvain, Brussels, Belgium.,MRI unit, Department of medical imaging, Cliniques Universitaires Saint-Luc, Brussels, Belgium
| | - Frank Peeters
- MRI unit, Department of medical imaging, Cliniques Universitaires Saint-Luc, Brussels, Belgium
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Frank LR, Zahneisen B, Galinsky VL. JEDI: Joint Estimation Diffusion Imaging of macroscopic and microscopic tissue properties. Magn Reson Med 2020; 84:966-990. [PMID: 31916626 DOI: 10.1002/mrm.28141] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 11/12/2019] [Accepted: 11/30/2019] [Indexed: 11/07/2022]
Abstract
PURPOSE A new method for enhancing the sensitivity of diffusion MRI (dMRI) by combining the data from single (sPFG) and double (dPFG) pulsed field gradient experiments is presented. METHODS This method uses our JESTER framework to combine microscopic anisotropy information from dFPG experiments using a new method called diffusion tensor subspace imaging (DiTSI) to augment the macroscopic anisotropy information from sPFG data analyzed using our guided by entropy spectrum pathways method. This new method, called joint estimation diffusion imaging (JEDI), combines the sensitivity to macroscopic diffusion anisotropy of sPFG with the sensitivity to microscopic diffusion anisotropy of dPFG methods. RESULTS Its ability to produce significantly more detailed anisotropy maps and more complete fiber tracts than existing methods within both brain white matter (WM) and gray matter (GM) is demonstrated on normal human subjects on data collected using a novel fast, robust, and clinically feasible sPFG/dPFG acquisition. CONCLUSIONS The potential utility of this method is suggested by an initial demonstration of its ability to mitigate the problem of gyral bias. The capability of more completely characterizing the tissue structure and connectivity throughout the entire brain has broad implications for the utility and scope of dMRI in a wide range of research and clinical applications.
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Affiliation(s)
- Lawrence R Frank
- Center for Scientific Computation in Imaging, University of California at San Diego, La Jolla, CA, USA
- Center for Functional MRI, University of California at San Diego, La Jolla, CA, USA
| | | | - Vitaly L Galinsky
- Center for Scientific Computation in Imaging, University of California at San Diego, La Jolla, CA, USA
- Electrical and Computer Engineering Department, University of California at San Diego, La Jolla, CA, USA
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Anaby D, Morozov D, Seroussi I, Hametner S, Sochen N, Cohen Y. Single- and double-Diffusion encoding MRI for studying ex vivo apparent axon diameter distribution in spinal cord white matter. NMR IN BIOMEDICINE 2019; 32:e4170. [PMID: 31573745 DOI: 10.1002/nbm.4170] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 07/28/2019] [Accepted: 07/31/2019] [Indexed: 06/10/2023]
Abstract
Mapping average axon diameter (AAD) and axon diameter distribution (ADD) in neuronal tissues non-invasively is a challenging task that may have a tremendous effect on our understanding of the normal and diseased central nervous system (CNS). Water diffusion is used to probe microstructure in neuronal tissues, however, the different water populations and barriers that are present in these tissues turn this into a complex task. Therefore, it is not surprising that recently we have witnessed a burst in the development of new approaches and models that attempt to obtain, non-invasively, detailed microstructural information in the CNS. In this work, we aim at challenging and comparing the microstructural information obtained from single diffusion encoding (SDE) with double diffusion encoding (DDE) MRI. We first applied SDE and DDE MR spectroscopy (MRS) on microcapillary phantoms and then applied SDE and DDE MRI on an ex vivo porcine spinal cord (SC), using similar experimental conditions. The obtained diffusion MRI data were fitted by the same theoretical model, assuming that the signal in every voxel can be approximated as the superposition of a Gaussian-diffusing component and a series of restricted components having infinite cylindrical geometries. The diffusion MRI results were then compared with histological findings. We found a good agreement between the fittings and the experimental data in white matter (WM) voxels of the SC in both diffusion MRI methods. The microstructural information and apparent AADs extracted from SDE MRI were found to be similar or somewhat larger than those extracted from DDE MRI especially when the diffusion time was set to 40 ms. The apparent ADDs extracted from SDE and DDE MRI show reasonable agreement but somewhat weaker correspondence was observed between the diffusion MRI results and histology. The apparent subtle differences between the microstructural information obtained from SDE and DDE MRI are briefly discussed.
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Affiliation(s)
- Debbie Anaby
- School of Chemistry, The Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel
- Department of Diagnostic Imaging, Sheba Medical Center, Tel HaShomer, Israel
| | - Darya Morozov
- School of Chemistry, The Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Inbar Seroussi
- School of Mathematical Sciences, The Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Simon Hametner
- Neuroimmunology Department, Center of Brain Research, Medical University of Vienna, Vienna, Austria
| | - Nir Sochen
- School of Mathematical Sciences, The Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel
- The Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Yoram Cohen
- School of Chemistry, The Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel
- The Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
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9
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Romascano D, Barakovic M, Rafael-Patino J, Dyrby TB, Thiran JP, Daducci A. ActiveAx ADD : Toward non-parametric and orientationally invariant axon diameter distribution mapping using PGSE. Magn Reson Med 2019; 83:2322-2330. [PMID: 31691378 DOI: 10.1002/mrm.28053] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 09/15/2019] [Accepted: 10/07/2019] [Indexed: 11/08/2022]
Abstract
PURPOSE Non-invasive axon diameter distribution (ADD) mapping using diffusion MRI is an ill-posed problem. Current ADD mapping methods require knowledge of axon orientation before performing the acquisition. Instead, ActiveAx uses a 3D sampling scheme to estimate the orientation from the signal, providing orientationally invariant estimates. The mean diameter is estimated instead of the distribution for the solution to be tractable. Here, we propose an extension (ActiveAxADD ) that provides non-parametric and orientationally invariant estimates of the whole distribution. THEORY The accelerated microstructure imaging with convex optimization (AMICO) framework accelerates mean diameter estimation using a linear formulation combined with Tikhonov regularization to stabilize the solution. Here, we implement a new formulation (ActiveAxADD ) that uses Laplacian regularization to provide robust estimates of the whole ADD. METHODS The performance of ActiveAxADD was evaluated using Monte Carlo simulations on synthetic white matter samples mimicking axon distributions reported in histological studies. RESULTS ActiveAxADD provided robust ADD reconstructions when considering the isolated intra-axonal signal. However, our formulation inherited some common microstructure imaging limitations. When accounting for the extra axonal compartment, estimated ADDs showed spurious peaks and increased variability because of the difficulty of disentangling intra and extra axonal contributions. CONCLUSION Laplacian regularization solves the ill-posedness regarding the intra axonal compartment. ActiveAxADD can potentially provide non-parametric and orientationally invariant ADDs from isolated intra-axonal signals. However, further work is required before ActiveAxADD can be applied to real data containing extra-axonal contributions, as disentangling the 2 compartment appears to be an overlooked challenge that affects microstructure imaging methods in general.
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Affiliation(s)
- David Romascano
- Signal Processing Laboratory (LTS5), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Vaud, Switzerland.,Danish Research Centre for Magnetic Resonance, Center for Functional and Diagnostic Imaging and Research, Copenhagen University Hospital Hvidovre, Hvidovre, Denmark
| | - Muhamed Barakovic
- Signal Processing Laboratory (LTS5), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Vaud, Switzerland
| | - Jonathan Rafael-Patino
- Signal Processing Laboratory (LTS5), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Vaud, Switzerland
| | - Tim Bjørn Dyrby
- Danish Research Centre for Magnetic Resonance, Center for Functional and Diagnostic Imaging and Research, Copenhagen University Hospital Hvidovre, Hvidovre, Denmark.,Department of Applied Mathematics and Computer Science, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Jean-Philippe Thiran
- Signal Processing Laboratory (LTS5), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Vaud, Switzerland.,Department of Radiology, University Hospital Center (CHUV) and University of Lausanne (UNIL), Lausanne, Vaud, Switzerland
| | - Alessandro Daducci
- Signal Processing Laboratory (LTS5), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Vaud, Switzerland.,Department of Radiology, University Hospital Center (CHUV) and University of Lausanne (UNIL), Lausanne, Vaud, Switzerland.,Computer Science Department, University of Verona, Verona, Italy
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Duchêne G, Abarca‐Quinones J, Leclercq I, Duprez T, Peeters F. Insights into tissue microstructure using a double diffusion encoding sequence on a clinical scanner: Validation and application to experimental tumor models. Magn Reson Med 2019; 83:1263-1276. [DOI: 10.1002/mrm.28012] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 09/03/2019] [Accepted: 09/05/2019] [Indexed: 12/15/2022]
Affiliation(s)
| | - Jorge Abarca‐Quinones
- Université Catholique de Louvain Brussels Belgium
- Cliniques Universitaires Saint‐Luc Brussels Belgium
| | - Isabelle Leclercq
- Université Catholique de Louvain Brussels Belgium
- Cliniques Universitaires Saint‐Luc Brussels Belgium
| | - Thierry Duprez
- Université Catholique de Louvain Brussels Belgium
- Cliniques Universitaires Saint‐Luc Brussels Belgium
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11
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Novikov DS, Fieremans E, Jespersen SN, Kiselev VG. Quantifying brain microstructure with diffusion MRI: Theory and parameter estimation. NMR IN BIOMEDICINE 2019; 32:e3998. [PMID: 30321478 PMCID: PMC6481929 DOI: 10.1002/nbm.3998] [Citation(s) in RCA: 248] [Impact Index Per Article: 49.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 06/11/2018] [Accepted: 06/28/2018] [Indexed: 05/18/2023]
Abstract
We review, systematize and discuss models of diffusion in neuronal tissue, by putting them into an overarching physical context of coarse-graining over an increasing diffusion length scale. From this perspective, we view research on quantifying brain microstructure as occurring along three major avenues. The first avenue focusses on transient, or time-dependent, effects in diffusion. These effects signify the gradual coarse-graining of tissue structure, which occurs qualitatively differently in different brain tissue compartments. We show that transient effects contain information about the relevant length scales for neuronal tissue, such as the packing correlation length for neuronal fibers, as well as the degree of structural disorder along the neurites. The second avenue corresponds to the long-time limit, when the observed signal can be approximated as a sum of multiple nonexchanging anisotropic Gaussian components. Here, the challenge lies in parameter estimation and in resolving its hidden degeneracies. The third avenue employs multiple diffusion encoding techniques, able to access information not contained in the conventional diffusion propagator. We conclude with our outlook on future directions that could open exciting possibilities for designing quantitative markers of tissue physiology and pathology, based on methods of studying mesoscopic transport in disordered systems.
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Affiliation(s)
- Dmitry S. Novikov
- Center for Biomedical Imaging, Department of Radiology, NYU School of Medicine, New York, NY, USA
| | - Els Fieremans
- Center for Biomedical Imaging, Department of Radiology, NYU School of Medicine, New York, NY, USA
| | - Sune N. Jespersen
- CFIN/MINDLab, Department of Clinical Medicine and Department of Physics and Astronomy, Aarhus University, Aarhus, Denmark
| | - Valerij G. Kiselev
- Medical Physics, Deptartment of Radiology, Faculty of Medicine, University of Freiburg, Germany
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Along-axon diameter variation and axonal orientation dispersion revealed with 3D electron microscopy: implications for quantifying brain white matter microstructure with histology and diffusion MRI. Brain Struct Funct 2019; 224:1469-1488. [PMID: 30790073 DOI: 10.1007/s00429-019-01844-6] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 02/01/2019] [Indexed: 10/27/2022]
Abstract
Tissue microstructure modeling of diffusion MRI signal is an active research area striving to bridge the gap between macroscopic MRI resolution and cellular-level tissue architecture. Such modeling in neuronal tissue relies on a number of assumptions about the microstructural features of axonal fiber bundles, such as the axonal shape (e.g., perfect cylinders) and the fiber orientation dispersion. However, these assumptions have not yet been validated by sufficiently high-resolution 3-dimensional histology. Here, we reconstructed sequential scanning electron microscopy images in mouse brain corpus callosum, and introduced a random-walker (RaW)-based algorithm to rapidly segment individual intra-axonal spaces and myelin sheaths of myelinated axons. Confirmed by a segmentation based on human annotations initiated with conventional machine-learning-based carving, our semi-automatic algorithm is reliable and less time-consuming. Based on the segmentation, we calculated MRI-relevant estimates of size-related parameters (inner axonal diameter, its distribution, along-axon variation, and myelin g-ratio), and orientation-related parameters (fiber orientation distribution and its rotational invariants; dispersion angle). The reported dispersion angle is consistent with previous 2-dimensional histology studies and diffusion MRI measurements, while the reported diameter exceeds those in other mouse brain studies. Furthermore, we calculated how these quantities would evolve in actual diffusion MRI experiments as a function of diffusion time, thereby providing a coarse-graining window on the microstructure, and showed that the orientation-related metrics have negligible diffusion time-dependence over clinical and pre-clinical diffusion time ranges. However, the MRI-measured inner axonal diameters, dominated by the widest cross sections, effectively decrease with diffusion time by ~ 17% due to the coarse-graining over axonal caliber variations. Furthermore, our 3d measurement showed that there is significant variation of the diameter along the axon. Hence, fiber orientation dispersion estimated from MRI should be relatively stable, while the "apparent" inner axonal diameters are sensitive to experimental settings, and cannot be modeled by perfectly cylindrical axons.
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13
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Johnson CDL, Zuidema JM, Kearns KR, Maguire AB, Desmond GP, Thompson DM, Gilbert RJ. The Effect of Electrospun Fiber Diameter on Astrocyte-Mediated Neurite Guidance and Protection. ACS APPLIED BIO MATERIALS 2018; 2:104-117. [PMID: 31061987 DOI: 10.1021/acsabm.8b00432] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The topography of electrospun fiber scaffolds modifies astrocytes toward in vivo-like morphologies and behaviors. However, little is known about how electrospun fiber diameter influences astrocyte behavior. In this work, aligned fibers with two distinct nanoscale fiber diameters (808 and 386 nm) were prepared, and the astrocyte response was measured over time. Astrocytes on the large diameter fibers showed significantly increased elongation as early as 2 h after seeding and remained significantly more elongated for up to 4 days compared to those on small diameter fibers. Astrocytes extending along larger diameter fibers were better equipped to support long neurite outgrowth from dorsal root ganglia neurons, and neurite outgrowth along these astrocytes was less branched than outgrowth along astrocytes cultured on small diameter fibers. The differences in astrocyte shape observed on the small or large diameter fibers did not translate into differences in GLT-1, GFAP, or GLAST protein expression. Thus, different fiber diameters were unable to influence astrocyte protein expression uniquely. Nevertheless, astrocytes cultured in either small or large fibers significantly increased their expression of GLT-1 compared to astrocytes cultured on nonfiber (film) controls. Fibrous-induced increases in astrocyte GLT-1 expression protected astrocyte/neuron cocultures from toxicity generated by high extracellular glutamate. Alternatively, astrocytes/neurons cultured on films were less able to protect these cells from culture conditions consisting of high glutamate levels. Biomaterials, such as the fibrous materials presented here, may help stimulate astrocytes to increase GLT-1 expression and uptake more glutamate, since astrocytes are less likely to uptake glutamate in neurodegenerative pathologies or following central nervous system injury.
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Affiliation(s)
- Christopher D L Johnson
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 Eighth Street, Troy, New York 12180-3590, United States.,Department of Biomedical Engineering, Rensselaer Polytechnic Institute, 110 Eighth Street, Troy, New York 12180-3590, United States
| | - Jonathan M Zuidema
- Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Dr., La Jolla, California 92093, United States
| | - Kathryn R Kearns
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 Eighth Street, Troy, New York 12180-3590, United States.,Department of Biomedical Engineering, Rensselaer Polytechnic Institute, 110 Eighth Street, Troy, New York 12180-3590, United States
| | - Alianna B Maguire
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, 110 Eighth Street, Troy, New York 12180-3590, United States
| | - Gregory P Desmond
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, 110 Eighth Street, Troy, New York 12180-3590, United States
| | - Deanna M Thompson
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 Eighth Street, Troy, New York 12180-3590, United States.,Department of Biomedical Engineering, Rensselaer Polytechnic Institute, 110 Eighth Street, Troy, New York 12180-3590, United States
| | - Ryan J Gilbert
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 Eighth Street, Troy, New York 12180-3590, United States.,Department of Biomedical Engineering, Rensselaer Polytechnic Institute, 110 Eighth Street, Troy, New York 12180-3590, United States
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14
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Lee HH, Fieremans E, Novikov DS. What dominates the time dependence of diffusion transverse to axons: Intra- or extra-axonal water? Neuroimage 2018; 182:500-510. [PMID: 29253652 PMCID: PMC6004237 DOI: 10.1016/j.neuroimage.2017.12.038] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2017] [Revised: 11/18/2017] [Accepted: 12/13/2017] [Indexed: 12/31/2022] Open
Abstract
Brownian motion of water molecules provides an essential length scale, the diffusion length, commensurate with cell dimensions in biological tissues. Measuring the diffusion coefficient as a function of diffusion time makes in vivo diffusion MRI uniquely sensitive to the cellular features about three orders of magnitude below imaging resolution. However, there is a longstanding debate, regarding which contribution - intra- or extra-cellular - is more relevant in the overall time-dependence of the MRI-derived diffusion metrics. Here we resolve this debate in the human brain white matter. By varying not just the diffusion time, but also the gradient pulse duration of a standard diffusion MRI sequence, we identify a functional form of the measured time-dependent diffusion coefficient transverse to white matter tracts in 10 healthy volunteers. This specific functional form is shown to originate from the extra-axonal space, and provides estimates of the fiber packing correlation length for axons in a bundle. Our results offer a metric for the outer axonal diameter, a promising candidate marker for demyelination in neurodegenerative diseases. From the methodological perspective, our analysis demonstrates how competing models, which describe different physics yet interpolate standard measurements equally well, can be distinguished based on their prediction for an independent "orthogonal" measurement.
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Affiliation(s)
- Hong-Hsi Lee
- Center for Biomedical Imaging, Department of Radiology, NYU School of Medicine, New York, NY 10016, United States.
| | - Els Fieremans
- Center for Biomedical Imaging, Department of Radiology, NYU School of Medicine, New York, NY 10016, United States
| | - Dmitry S Novikov
- Center for Biomedical Imaging, Department of Radiology, NYU School of Medicine, New York, NY 10016, United States
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15
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Komlosh ME, Benjamini D, Hutchinson EB, King S, Haber M, Avram AV, Holtzclaw LA, Desai A, Pierpaoli C, Basser PJ. Using double pulsed-field gradient MRI to study tissue microstructure in traumatic brain injury (TBI). MICROPOROUS AND MESOPOROUS MATERIALS : THE OFFICIAL JOURNAL OF THE INTERNATIONAL ZEOLITE ASSOCIATION 2018; 269:156-159. [PMID: 30337835 PMCID: PMC6188654 DOI: 10.1016/j.micromeso.2017.05.030] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Double pulsed-field gradient (dPFG) MRI is proposed as a new sensitive tool to detect and characterize tissue microstructure following diffuse axonal injury. In this study dPFG MRI was used to estimate apparent mean axon diameter in a diffuse axonal injury animal model and in healthy fixed mouse brain. Histological analysis was used to verify the presence of the injury detected by MRI.
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Affiliation(s)
- Michal E Komlosh
- Section on Quantitative Imaging and Tissue Sciences, NICHD, National Institutes of Health, Bethesda, MD, USA
- Center for Neuroscience and Regenerative Medicine, Uniform Service University of the Health Sciences, Bethesda, MD, USA
| | - Dan Benjamini
- Section on Quantitative Imaging and Tissue Sciences, NICHD, National Institutes of Health, Bethesda, MD, USA
| | - Elizabeth B Hutchinson
- Section on Quantitative Imaging and Tissue Sciences, NICHD, National Institutes of Health, Bethesda, MD, USA
- Center for Neuroscience and Regenerative Medicine, Uniform Service University of the Health Sciences, Bethesda, MD, USA
| | - Sarah King
- Section on Quantitative Imaging and Tissue Sciences, NICHD, National Institutes of Health, Bethesda, MD, USA
- Center for Neuroscience and Regenerative Medicine, Uniform Service University of the Health Sciences, Bethesda, MD, USA
| | - Margalit Haber
- Department of Neurology, University of Pennsylvania, Philadelphia, PA, USA
| | - Alexandru V Avram
- Section on Quantitative Imaging and Tissue Sciences, NICHD, National Institutes of Health, Bethesda, MD, USA
| | - Lynne A Holtzclaw
- Microscopy and Imaging Core, NICHD, National Institutes of Health, Bethesda, MD, USA
| | - Abhishek Desai
- Laboratory of Molecular Signaling, NIAAA, National Institutes of Health, Rockville, MD, USA
| | - Carlo Pierpaoli
- Section on Quantitative Imaging and Tissue Sciences, NICHD, National Institutes of Health, Bethesda, MD, USA
| | - Peter J Basser
- Section on Quantitative Imaging and Tissue Sciences, NICHD, National Institutes of Health, Bethesda, MD, USA
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16
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Novikov DS, Kiselev VG, Jespersen SN. On modeling. Magn Reson Med 2018; 79:3172-3193. [PMID: 29493816 PMCID: PMC5905348 DOI: 10.1002/mrm.27101] [Citation(s) in RCA: 213] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 12/22/2017] [Accepted: 01/01/2018] [Indexed: 01/17/2023]
Abstract
Mapping tissue microstructure with MRI holds great promise as a noninvasive window into tissue organization at the cellular level. Having originated within the realm of diffusion NMR in the late 1970s, this field is experiencing an exponential growth in the number of publications. At the same time, model-based approaches are also increasingly incorporated into advanced MRI acquisition and reconstruction techniques. However, after about two decades of intellectual and financial investment, microstructural mapping has yet to find a single commonly accepted clinical application. Here, we suggest that slow progress in clinical translation may signify unresolved fundamental problems. We outline such problems and related practical pitfalls, as well as review strategies for developing and validating tissue microstructure models, to provoke a discussion on how to bridge the gap between our scientific aspirations and the clinical reality. We argue for recalibrating the efforts of our community toward a more systematic focus on fundamental research aimed at identifying relevant degrees of freedom affecting the measured MR signal. Such a focus is essential for realizing the truly revolutionary potential of noninvasive three-dimensional in vivo microstructural mapping.
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Affiliation(s)
- Dmitry S Novikov
- Bernard and Irene Schwartz Center for Biomedical Imaging, Department of Radiology, New York University School of Medicine, New York, New York, USA
| | - Valerij G Kiselev
- Department of Radiology, Medical Physics, University Medical Center Freiburg, Faculty of Medicine, Freiburg, Germany
| | - Sune N Jespersen
- CFIN/MINDLab, Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Physics and Astronomy, Aarhus University, Aarhus, Denmark
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17
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By S, Xu J, Box BA, Bagnato FR, Smith SA. Multi-compartmental diffusion characterization of the human cervical spinal cord in vivo using the spherical mean technique. NMR IN BIOMEDICINE 2018; 31:e3894. [PMID: 29388719 PMCID: PMC5854548 DOI: 10.1002/nbm.3894] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 12/12/2017] [Accepted: 12/16/2017] [Indexed: 05/02/2023]
Abstract
The purpose of this work was to evaluate the feasibility and reproducibility of the spherical mean technique (SMT), a multi-compartmental diffusion model, in the spinal cord of healthy controls, and to assess its ability to improve spinal cord characterization in multiple sclerosis (MS) patients at 3 T. SMT was applied in the cervical spinal cord of eight controls and six relapsing-remitting MS patients. SMT provides an elegant framework to model the apparent axonal volume fraction vax , intrinsic diffusivity Dax , and extra-axonal transverse diffusivity Dex_perp (which is estimated as a function of vax and Dax ) without confounds related to complex fiber orientation distribution that reside in diffusion MRI modeling. SMT's reproducibility was assessed with two different scans within a month, and SMT-derived indices in healthy and MS cohorts were compared. The influence of acquisition scheme on SMT was also evaluated. SMT's vax , Dax , and Dex_perp measurements all showed high reproducibility. A decrease in vax was observed at the site of lesions and normal appearing white matter (p < 0.05), and trends towards a decreased Dax and increased Dex_perp were seen. Importantly, a twofold reduction in acquisition yielded similarly high accuracy with SMT. SMT provides a fast, reproducible, and accurate method to improve characterization of the cervical spinal cord, and may have clinical potential for MS patients.
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Affiliation(s)
- Samantha By
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
- Vanderbilt University Institute of Imaging Science, Vanderbilt University Medical Center, Nashville, TN, USA
- Philips Healthcare, Gainesville, FL, USA
| | - Junzhong Xu
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
- Vanderbilt University Institute of Imaging Science, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Radiology and Radiological Sciences, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Bailey A. Box
- Vanderbilt University Institute of Imaging Science, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Francesca R. Bagnato
- Department of Neurology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Seth A. Smith
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
- Vanderbilt University Institute of Imaging Science, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Radiology and Radiological Sciences, Vanderbilt University Medical Center, Nashville, TN, USA
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18
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Nilsson M, Lasič S, Drobnjak I, Topgaard D, Westin C. Resolution limit of cylinder diameter estimation by diffusion MRI: The impact of gradient waveform and orientation dispersion. NMR IN BIOMEDICINE 2017; 30:e3711. [PMID: 28318071 PMCID: PMC5485041 DOI: 10.1002/nbm.3711] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Revised: 01/16/2017] [Accepted: 01/20/2017] [Indexed: 05/20/2023]
Abstract
Diffusion MRI has been proposed as a non-invasive technique for axonal diameter mapping. However, accurate estimation of small diameters requires strong gradients, which is a challenge for the transition of the technique from preclinical to clinical MRI scanners, since these have weaker gradients. In this work, we develop a framework to estimate the lower bound for accurate diameter estimation, which we refer to as the resolution limit. We analyse only the contribution from the intra-axonal space and assume that axons can be represented by impermeable cylinders. To address the growing interest in using techniques for diffusion encoding that go beyond the conventional single diffusion encoding (SDE) sequence, we present a generalised analysis capable of predicting the resolution limit regardless of the gradient waveform. Using this framework, waveforms were optimised to minimise the resolution limit. The results show that, for parallel cylinders, the SDE experiment is optimal in terms of yielding the lowest possible resolution limit. In the presence of orientation dispersion, diffusion encoding sequences with square-wave oscillating gradients were optimal. The resolution limit for standard clinical MRI scanners (maximum gradient strength 60-80 mT/m) was found to be between 4 and 8 μm, depending on the noise levels and the level of orientation dispersion. For scanners with a maximum gradient strength of 300 mT/m, the limit was reduced to between 2 and 5 μm.
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Affiliation(s)
- Markus Nilsson
- Clinical Sciences Lund, Department of RadiologyLund UniversityLundSweden
| | | | | | - Daniel Topgaard
- Division of Physical Chemistry, Department of ChemistryLund UniversityLundSweden
| | - Carl‐Fredrik Westin
- Department of Biomedical EngineeringLinköping UniversityLinköpingSweden
- Brigham and Women's HospitalHarvard Medical SchoolBostonMAUSA
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19
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Benjamini D, Komlosh ME, Basser PJ. Imaging Local Diffusive Dynamics Using Diffusion Exchange Spectroscopy MRI. PHYSICAL REVIEW LETTERS 2017; 118:158003. [PMID: 28452522 PMCID: PMC11079612 DOI: 10.1103/physrevlett.118.158003] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Indexed: 06/07/2023]
Abstract
The movement of water between microenvironments presents a central challenge in the physics of soft matter and porous media. Diffusion exchange spectroscopy (DEXSY) is a powerful 2D nuclear magnetic resonance method for measuring such exchange, yet it is rarely used because of its long scan time requirements. Moreover, it has never been combined with magnetic resonance imaging (MRI). Using probability theory, we vastly reduce the required data, making DEXSY MRI feasible for the first time. Experiments are performed on a composite nerve tissue phantom with restricted and free water-exchanging compartments.
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Affiliation(s)
- Dan Benjamini
- Section on Quantitative Imaging and Tissue Sciences, NICHD, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Michal E. Komlosh
- Section on Quantitative Imaging and Tissue Sciences, NICHD, National Institutes of Health, Bethesda, Maryland 20892, USA
- Center for Neuroscience and Regenerative Medicine, Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland 20892, USA
| | - Peter J. Basser
- Section on Quantitative Imaging and Tissue Sciences, NICHD, National Institutes of Health, Bethesda, Maryland 20892, USA
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20
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Morozov D, Tal I, Pisanty O, Shani E, Cohen Y. Studying microstructure and microstructural changes in plant tissues by advanced diffusion magnetic resonance imaging techniques. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:2245-2257. [PMID: 28398563 PMCID: PMC5447889 DOI: 10.1093/jxb/erx106] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
As sessile organisms, plants must respond to the environment by adjusting their growth and development. Most of the plant body is formed post-embryonically by continuous activity of apical and lateral meristems. The development of lateral adventitious roots is a complex process, and therefore the development of methods that can visualize, non-invasively, the plant microstructure and organ initiation that occur during growth and development is of paramount importance. In this study, relaxation-based and advanced diffusion magnetic resonance imaging (MRI) methods including diffusion tensor (DTI), q-space diffusion imaging (QSI), and double-pulsed-field-gradient (d-PFG) MRI, at 14.1 T, were used to characterize the hypocotyl microstructure and the microstructural changes that occurred during the development of lateral adventitious roots in tomato. Better contrast was observed in relaxation-based MRI using higher in-plane resolution but this also resulted in a significant reduction in the signal-to-noise ratio of the T2-weighted MR images. Diffusion MRI revealed that water diffusion is highly anisotropic in the vascular cylinder. QSI and d-PGSE MRI showed that in the vascular cylinder some of the cells have sizes in the range of 6-10 μm. The MR images captured cell reorganization during adventitious root formation in the periphery of the primary vascular bundles, adjacent to the xylem pole that broke through the cortex and epidermis layers. This study demonstrates that MRI and diffusion MRI methods allow the non-invasive study of microstructural features of plants, and enable microstructural changes associated with adventitious root formation to be followed.
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Affiliation(s)
- Darya Morozov
- School of Chemistry, The Sackler Faculty of Exact Sciences, and
| | - Iris Tal
- Department of Molecular Biology and Ecology of Plants, Tel Aviv University, Ramat Aviv, Tel Aviv 66978, Israel
| | - Odelia Pisanty
- Department of Molecular Biology and Ecology of Plants, Tel Aviv University, Ramat Aviv, Tel Aviv 66978, Israel
| | - Eilon Shani
- Department of Molecular Biology and Ecology of Plants, Tel Aviv University, Ramat Aviv, Tel Aviv 66978, Israel
| | - Yoram Cohen
- School of Chemistry, The Sackler Faculty of Exact Sciences, and
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21
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Cohen Y, Anaby D, Morozov D. Diffusion MRI of the spinal cord: from structural studies to pathology. NMR IN BIOMEDICINE 2017; 30:e3592. [PMID: 27598689 DOI: 10.1002/nbm.3592] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 06/01/2016] [Accepted: 07/05/2016] [Indexed: 05/27/2023]
Abstract
Diffusion MRI is extensively used to study brain microarchitecture and pathologies, and water diffusion appears highly anisotropic in the white matter (WM) of the spinal cord (SC). Despite these facts, the use of diffusion MRI to study the SC, which has increased in recent years, is much less common than that in the brain. In the present review, after a brief outline of early studies of diffusion MRI (DWI) and diffusion tensor MRI (DTI) of the SC, we provide a short survey on DTI and on diffusion MRI methods beyond the tensor that have been used to study SC microstructure and pathologies. After introducing the porous view of WM and describing the q-space approach and q-space diffusion MRI (QSI), we describe other methodologies that can be applied to study the SC. Selected applications of the use of DTI, QSI, and other more advanced diffusion MRI methods to study SC microstructure and pathologies are presented, with some emphasis on the use of less conventional diffusion methodologies. Because of length constraints, we concentrate on structural studies and on a few selected pathologies. Examples of the use of diffusion MRI to study dysmyelination, demyelination as in experimental autoimmune encephalomyelitis and multiple sclerosis, amyotrophic lateral sclerosis, and traumatic SC injury are presented. We conclude with a brief summary and a discussion of challenges and future directions for diffusion MRI of the SC. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Yoram Cohen
- The Sackler School of Chemistry, The Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel
- The Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Debbie Anaby
- The Sackler School of Chemistry, The Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Darya Morozov
- The Sackler School of Chemistry, The Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel
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22
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Komlosh ME, Benjamini D, Barnett AS, Schram V, Horkay F, Avram AV, Basser PJ. Anisotropic phantom to calibrate high-q diffusion MRI methods. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2017; 275:19-28. [PMID: 27951427 PMCID: PMC5325680 DOI: 10.1016/j.jmr.2016.11.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 11/29/2016] [Accepted: 11/29/2016] [Indexed: 05/30/2023]
Abstract
A silicon oil-filled glass capillary array is proposed as an anisotropic diffusion MRI phantom. Together with a computational/theoretical pipeline these provide a gold standard for calibrating and validating high-q diffusion MRI experiments. The phantom was used to test high angular resolution diffusion imaging (HARDI) and double pulsed-field gradient (d-PFG) MRI acquisition schemes. MRI-based predictions of microcapillary diameter using both acquisition schemes were compared with results from optical microscopy. This phantom design can be used for quality control and quality assurance purposes and for testing and validating proposed microstructure imaging experiments and the processing pipelines used to analyze them.
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Affiliation(s)
- M E Komlosh
- Section on Quantitative Imaging and Tissue Sciences, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA; Center for Neuroscience and Regenerative Medicine, The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc, Bethesda, MD, USA.
| | - D Benjamini
- Section on Quantitative Imaging and Tissue Sciences, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - A S Barnett
- Section on Quantitative Imaging and Tissue Sciences, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - V Schram
- Microscopy and Imaging Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - F Horkay
- Section on Quantitative Imaging and Tissue Sciences, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - A V Avram
- Section on Quantitative Imaging and Tissue Sciences, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - P J Basser
- Section on Quantitative Imaging and Tissue Sciences, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
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23
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Benjamini D, Komlosh ME, Holtzclaw LA, Nevo U, Basser PJ. White matter microstructure from nonparametric axon diameter distribution mapping. Neuroimage 2016; 135:333-44. [PMID: 27126002 DOI: 10.1016/j.neuroimage.2016.04.052] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 03/18/2016] [Accepted: 04/21/2016] [Indexed: 12/31/2022] Open
Abstract
We report the development of a double diffusion encoding (DDE) MRI method to estimate and map the axon diameter distribution (ADD) within an imaging volume. A variety of biological processes, ranging from development to disease and trauma, may lead to changes in the ADD in the central and peripheral nervous systems. Unlike previously proposed methods, this ADD experimental design and estimation framework employs a more general, nonparametric approach, without a priori assumptions about the underlying form of the ADD, making it suitable to analyze abnormal tissue. In the current study, this framework was used on an ex vivo ferret spinal cord, while emphasizing the way in which the ADD can be weighted by either the number or the volume of the axons. The different weightings, which result in different spatial contrasts, were considered throughout this work. DDE data were analyzed to derive spatially resolved maps of average axon diameter, ADD variance, and extra-axonal volume fraction, along with a novel sub-micron restricted structures map. The morphological information contained in these maps was then used to segment white matter into distinct domains by using a proposed k-means clustering algorithm with spatial contiguity and left-right symmetry constraints, resulting in identifiable white matter tracks. The method was validated by comparing histological measures to the estimated ADDs using a quantitative similarity metric, resulting in good agreement. With further acquisition acceleration and experimental parameters adjustments, this ADD estimation framework could be first used preclinically, and eventually clinically, enabling a wide range of neuroimaging applications for improved understanding of neurodegenerative pathologies and assessing microstructural changes resulting from trauma.
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Affiliation(s)
- Dan Benjamini
- Quantitative Imaging and Tissue Sciences, NICHD, National Institutes of Health, Bethesda, MD 20892, USA; Department of Biomedical Engineering, The Iby and Aladar Fleischman Faculty of Engineering, Tel-Aviv University, Tel-Aviv, Israel.
| | - Michal E Komlosh
- Quantitative Imaging and Tissue Sciences, NICHD, National Institutes of Health, Bethesda, MD 20892, USA; Center for Neuroscience and Regenerative Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
| | - Lynne A Holtzclaw
- Microscopy & Imaging Core, NICHD, National Institutes of Health, Bethesda, MD 20892, USA
| | - Uri Nevo
- Department of Biomedical Engineering, The Iby and Aladar Fleischman Faculty of Engineering, Tel-Aviv University, Tel-Aviv, Israel
| | - Peter J Basser
- Quantitative Imaging and Tissue Sciences, NICHD, National Institutes of Health, Bethesda, MD 20892, USA
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Xu J, Li H, Li K, Harkins KD, Jiang X, Xie J, Kang H, Dortch RD, Anderson AW, Does MD, Gore JC. Fast and simplified mapping of mean axon diameter using temporal diffusion spectroscopy. NMR IN BIOMEDICINE 2016; 29:400-410. [PMID: 27077155 PMCID: PMC4832578 DOI: 10.1002/nbm.3484] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Mapping axon diameter is of interest for the potential diagnosis and monitoring of various neuronal pathologies. Advanced diffusion-weighted MRI methods have been developed to measure mean axon diameters non-invasively, but suffer major drawbacks that prevent their direct translation into clinical practice, such as complex non-linear data fitting and, more importantly, long scanning times that are usually not tolerable for most human subjects. In the current study, temporal diffusion spectroscopy using oscillating diffusion gradients was used to measure mean axon diameters with high sensitivity to small axons in the central nervous system. Axon diameters have been found to be correlated with a novel metric, DDR⊥ (the rate of dispersion of the perpendicular diffusion coefficient with gradient frequency), which is a model-free quantity that does not require complex data analyses and can be obtained from two diffusion coefficient measurements in clinically relevant times with conventional MRI machines. A comprehensive investigation including computer simulations and animal experiments ex vivo showed that measurements of DDR⊥ agree closely with histological data. In humans in vivo, DDR⊥ was also found to correlate well with reported mean axon diameters in human corpus callosum, and the total scan time was only about 8 min. In conclusion, DDR⊥ may have potential to serve as a fast, simple and model-free approach to map the mean axon diameter of white matter in clinics for assessing axon diameter changes.
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Affiliation(s)
- Junzhong Xu
- Institute of Imaging Science, Vanderbilt University, Nashville, TN, USA; Department of Radiology and Radiological Sciences, Vanderbilt University, Nashville, TN, USA; Department of Physics and Astronomy, Vanderbilt University, Nashville, TN, USA.
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25
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Drobnjak I, Zhang H, Ianuş A, Kaden E, Alexander DC. PGSE, OGSE, and sensitivity to axon diameter in diffusion MRI: Insight from a simulation study. Magn Reson Med 2016. [PMID: 25809657 DOI: 10.1002/mrm.25631/full] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
Abstract
PURPOSE To identify optimal pulsed gradient spin-echo (PGSE) and oscillating gradient spin-echo (OGSE) sequence settings for maximizing sensitivity to axon diameter in idealized and practical conditions. METHODS Simulations on a simple two-compartment white matter model (with nonpermeable cylinders) are used to investigate a wide space of clinically plausible PGSE and OGSE sequence parameters with trapezoidal diffusion gradient waveforms. Signal sensitivity is measured as a derivative of the signal with respect to axon diameter. Models of parallel and dispersed fibers are investigated separately to represent idealized and practical conditions. RESULTS Simulations show that, for the simple case of gradients perfectly perpendicular to straight parallel fibers, PGSE always gives maximum sensitivity. However, in real-world scenarios where fibers have unknown and dispersed orientation, low-frequency OGSE provides higher sensitivity. Maximum sensitivity results show that on current clinical scanners (Gmax = 60 mT/m, signal to noise ratio (SNR) = 20) axon diameters below 6 µm are indistinguishable from zero. Scanners with stronger gradient systems such as the Massachusetts General Hospital (MGH) Connectom scanner (Gmax = 300 mT/m) can extend this sensitivity limit down to 2-3 µm, probing a much greater proportion of the underlying axon diameter distribution. CONCLUSION Low-frequency OGSE provides additional sensitivity to PGSE in practical situations. OGSE is particularly advantageous for systems with high performance gradients.
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Affiliation(s)
- Ivana Drobnjak
- Department of Computer Science and Centre for Medical Image Computing, University College London (UCL), London, UK
| | - Hui Zhang
- Department of Computer Science and Centre for Medical Image Computing, University College London (UCL), London, UK
| | - Andrada Ianuş
- Department of Computer Science and Centre for Medical Image Computing, University College London (UCL), London, UK
| | - Enrico Kaden
- Department of Computer Science and Centre for Medical Image Computing, University College London (UCL), London, UK
| | - Daniel C Alexander
- Department of Computer Science and Centre for Medical Image Computing, University College London (UCL), London, UK
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Benjamini D, Basser PJ. Joint radius-length distribution as a measure of anisotropic pore eccentricity: an experimental and analytical framework. J Chem Phys 2015; 141:214202. [PMID: 25481136 DOI: 10.1063/1.4901134] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In this work, we present an experimental design and analytical framework to measure the nonparametric joint radius-length (R-L) distribution of an ensemble of parallel, finite cylindrical pores, and more generally, the eccentricity distribution of anisotropic pores. Employing a novel 3D double pulsed-field gradient acquisition scheme, we first obtain both the marginal radius and length distributions of a population of cylindrical pores and then use these to constrain and stabilize the estimate of the joint radius-length distribution. Using the marginal distributions as constraints allows the joint R-L distribution to be reconstructed from an underdetermined system (i.e., more variables than equations), which requires a relatively small and feasible number of MR acquisitions. Three simulated representative joint R-L distribution phantoms corrupted by different noise levels were reconstructed to demonstrate the process, using this new framework. As expected, the broader the peaks in the joint distribution, the less stable and more sensitive to noise the estimation of the marginal distributions. Nevertheless, the reconstruction of the joint distribution is remarkably robust to increases in noise level; we attribute this characteristic to the use of the marginal distributions as constraints. Axons are known to exhibit local compartment eccentricity variations upon injury; the extent of the variations depends on the severity of the injury. Nonparametric estimation of the eccentricity distribution of injured axonal tissue is of particular interest since generally one cannot assume a parametric distribution a priori. Reconstructing the eccentricity distribution may provide vital information about changes resulting from injury or that occurred during development.
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Affiliation(s)
- Dan Benjamini
- Section on Tissue Biophysics and Biomimetics, PPITS, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, Maryland 20892-5772, USA
| | - Peter J Basser
- Section on Tissue Biophysics and Biomimetics, PPITS, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, Maryland 20892-5772, USA
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Drobnjak I, Zhang H, Ianuş A, Kaden E, Alexander DC. PGSE, OGSE, and sensitivity to axon diameter in diffusion MRI: Insight from a simulation study. Magn Reson Med 2015; 75:688-700. [PMID: 25809657 PMCID: PMC4975609 DOI: 10.1002/mrm.25631] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Revised: 12/19/2014] [Accepted: 01/05/2015] [Indexed: 11/27/2022]
Abstract
Purpose To identify optimal pulsed gradient spin‐echo (PGSE) and oscillating gradient spin‐echo (OGSE) sequence settings for maximizing sensitivity to axon diameter in idealized and practical conditions. Methods Simulations on a simple two‐compartment white matter model (with nonpermeable cylinders) are used to investigate a wide space of clinically plausible PGSE and OGSE sequence parameters with trapezoidal diffusion gradient waveforms. Signal sensitivity is measured as a derivative of the signal with respect to axon diameter. Models of parallel and dispersed fibers are investigated separately to represent idealized and practical conditions. Results Simulations show that, for the simple case of gradients perfectly perpendicular to straight parallel fibers, PGSE always gives maximum sensitivity. However, in real‐world scenarios where fibers have unknown and dispersed orientation, low‐frequency OGSE provides higher sensitivity. Maximum sensitivity results show that on current clinical scanners (Gmax = 60 mT/m, signal to noise ratio (SNR) = 20) axon diameters below 6 µm are indistinguishable from zero. Scanners with stronger gradient systems such as the Massachusetts General Hospital (MGH) Connectom scanner (Gmax = 300 mT/m) can extend this sensitivity limit down to 2–3 µm, probing a much greater proportion of the underlying axon diameter distribution. Conclusion Low‐frequency OGSE provides additional sensitivity to PGSE in practical situations. OGSE is particularly advantageous for systems with high performance gradients. Magn Reson Med 75:688–700, 2016. © 2015 The Authors Magnetic Resonance in Medicine published by Wiley Periodicals, Inc. on behalf of International Society for Magnetic Resonance in Medicine. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
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Affiliation(s)
- Ivana Drobnjak
- Department of Computer Science and Centre for Medical Image Computing, University College London (UCL), London, UK
| | - Hui Zhang
- Department of Computer Science and Centre for Medical Image Computing, University College London (UCL), London, UK
| | - Andrada Ianuş
- Department of Computer Science and Centre for Medical Image Computing, University College London (UCL), London, UK
| | - Enrico Kaden
- Department of Computer Science and Centre for Medical Image Computing, University College London (UCL), London, UK
| | - Daniel C Alexander
- Department of Computer Science and Centre for Medical Image Computing, University College London (UCL), London, UK
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Xu J, Li H, Harkins KD, Jiang X, Xie J, Kang H, Does MD, Gore JC. Mapping mean axon diameter and axonal volume fraction by MRI using temporal diffusion spectroscopy. Neuroimage 2014; 103:10-19. [PMID: 25225002 PMCID: PMC4312203 DOI: 10.1016/j.neuroimage.2014.09.006] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Revised: 09/02/2014] [Accepted: 09/04/2014] [Indexed: 02/01/2023] Open
Abstract
Mapping mean axon diameter and intra-axonal volume fraction may have significant clinical potential because nerve conduction velocity is directly dependent on axon diameter, and several neurodegenerative diseases affect axons of specific sizes and alter axon counts. Diffusion-weighted MRI methods based on the pulsed gradient spin echo (PGSE) sequence have been reported to be able to assess axon diameter and volume fraction non-invasively. However, due to the relatively long diffusion times used, e.g. >20ms, the sensitivity to small axons (diameter<2μm) is low, and the derived mean axon diameter has been reported to be overestimated. In the current study, oscillating gradient spin echo (OGSE) diffusion sequences with variable frequency gradients were used to assess rat spinal white matter tracts with relatively short effective diffusion times (1-5ms). In contrast to previous PGSE-based methods, the extra-axonal diffusion cannot be modeled as hindered (Gaussian) diffusion when short diffusion times are used. Appropriate frequency-dependent rates are therefore incorporated into our analysis and validated by histology-based computer simulation of water diffusion. OGSE data were analyzed to derive mean axon diameters and intra-axonal volume fractions of rat spinal white matter tracts (mean axon diameter of ~1.27-5.54μm). The estimated values were in good agreement with histology, including the small axon diameters (<2.5μm). This study establishes a framework for the quantification of nerve morphology using the OGSE method with high sensitivity to small axons.
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Affiliation(s)
- Junzhong Xu
- Institute of Imaging Science, Vanderbilt University, Nashville, TN 37232, USA; Department of Radiology and Radiological Sciences, Vanderbilt University, Nashville, TN 37232, USA; Department of Physics and Astronomy, Vanderbilt University, Nashville, TN 37232, USA.
| | - Hua Li
- Institute of Imaging Science, Vanderbilt University, Nashville, TN 37232, USA; Department of Physics and Astronomy, Vanderbilt University, Nashville, TN 37232, USA
| | - Kevin D Harkins
- Institute of Imaging Science, Vanderbilt University, Nashville, TN 37232, USA
| | - Xiaoyu Jiang
- Institute of Imaging Science, Vanderbilt University, Nashville, TN 37232, USA; Department of Radiology and Radiological Sciences, Vanderbilt University, Nashville, TN 37232, USA
| | - Jingping Xie
- Institute of Imaging Science, Vanderbilt University, Nashville, TN 37232, USA; Department of Radiology and Radiological Sciences, Vanderbilt University, Nashville, TN 37232, USA
| | - Hakmook Kang
- Department of Biostatistics, Vanderbilt University, Nashville, TN 37203, USA
| | - Mark D Does
- Institute of Imaging Science, Vanderbilt University, Nashville, TN 37232, USA; Department of Radiology and Radiological Sciences, Vanderbilt University, Nashville, TN 37232, USA; Department of Biomedical Engineering, Vanderbilt University, Nashville, TN 37232, USA
| | - John C Gore
- Institute of Imaging Science, Vanderbilt University, Nashville, TN 37232, USA; Department of Radiology and Radiological Sciences, Vanderbilt University, Nashville, TN 37232, USA; Department of Physics and Astronomy, Vanderbilt University, Nashville, TN 37232, USA; Department of Biomedical Engineering, Vanderbilt University, Nashville, TN 37232, USA; Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37232, USA
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29
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Benjamini D, Komlosh ME, Basser PJ, Nevo U. Nonparametric pore size distribution using d-PFG: comparison to s-PFG and migration to MRI. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2014; 246:36-45. [PMID: 25064269 PMCID: PMC7477619 DOI: 10.1016/j.jmr.2014.06.017] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Revised: 06/20/2014] [Accepted: 06/21/2014] [Indexed: 05/12/2023]
Abstract
Here we present the successful translation of a pore size distribution (PSD) estimation method from NMR to MRI. This approach is validated using a well-characterized MRI phantom consisting of stacked glass capillary arrays (GCA) having different diameters. By employing a double pulsed-field gradient (d-PFG) MRI sequence, this method overcomes several important theoretical and experimental limitations of previous single-PFG (s-PFG) based MRI methods by allowing the relative diffusion gradients' direction to vary. This feature adds an essential second dimension in the parameters space, which can potentially improve the reliability and stability of the PSD estimation. To infer PSDs from the MRI data in each voxel an inverse linear problem is solved in conjunction with the multiple correlation function (MCF) framework, which can account for arbitrary experimental parameters (e.g., long diffusion pulses). This scheme makes no a priori assumptions about the functional form of the underlying PSD. Creative use of region of interest (ROI) analysis allows us to create different underlying PSDs using the same GCA MRI phantom. We show that an s-PFG experiment on the GCA phantom fails to accurately reconstruct the size distribution, thus demonstrating the superiority of the d-PFG experiment. In addition, signal simulations corrupted by different noise levels were used to generate continuous and complex PSDs, which were then successfully reconstructed. Finally, owing to the reduced q- or b- values required to measure microscopic PSDs via d-PFG MRI, this method will be better suited to biomedical and clinical applications, in which gradient strength of scanners is limited.
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Affiliation(s)
- Dan Benjamini
- Section on Tissue Biophysics and Biomimetics, PPITS, Eunice Kennedy Shriver, National Institute of Child Health and Human Development, NIH, Bethesda, MD, USA; Department of Biomedical Engineering, The Iby and Aladar Fleischman Faculty of Engineering, Tel-Aviv University, Tel-Aviv, Israel
| | - Michal E Komlosh
- Section on Tissue Biophysics and Biomimetics, PPITS, Eunice Kennedy Shriver, National Institute of Child Health and Human Development, NIH, Bethesda, MD, USA; Center for Neuroscience and Regenerative Medicine, Uniform Service University of the Health Sciences, Bethesda, MD, USA
| | - Peter J Basser
- Section on Tissue Biophysics and Biomimetics, PPITS, Eunice Kennedy Shriver, National Institute of Child Health and Human Development, NIH, Bethesda, MD, USA
| | - Uri Nevo
- Department of Biomedical Engineering, The Iby and Aladar Fleischman Faculty of Engineering, Tel-Aviv University, Tel-Aviv, Israel.
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30
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Morozov D, Bar L, Sochen N, Cohen Y. Microstructural information from angular double-pulsed-field-gradient NMR: From model systems to nerves. Magn Reson Med 2014; 74:25-32. [DOI: 10.1002/mrm.25371] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2013] [Revised: 06/24/2014] [Accepted: 06/24/2014] [Indexed: 11/11/2022]
Affiliation(s)
- Darya Morozov
- School of Chemistry, The Raymond and Beverly Sackler Faculty of Exact Science, Tel Aviv University; Tel Aviv Israel
| | - Leah Bar
- School of Mathematical Sciences, The Raymond and Beverly Sackler Faculty of Exact Science, Tel Aviv University; Tel Aviv Israel
| | - Nir Sochen
- School of Mathematical Sciences, The Raymond and Beverly Sackler Faculty of Exact Science, Tel Aviv University; Tel Aviv Israel
| | - Yoram Cohen
- School of Chemistry, The Raymond and Beverly Sackler Faculty of Exact Science, Tel Aviv University; Tel Aviv Israel
- Sagol School of Neuroscience, Tel Aviv University; Tel Aviv Israel
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31
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Lam WW, Jbabdi S, Miller KL. A model for extra-axonal diffusion spectra with frequency-dependent restriction. Magn Reson Med 2014; 73:2306-20. [PMID: 25046481 PMCID: PMC4682484 DOI: 10.1002/mrm.25363] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Revised: 06/24/2014] [Accepted: 06/24/2014] [Indexed: 11/09/2022]
Abstract
PURPOSE In the brain, there is growing interest in using the temporal diffusion spectrum to characterize axonal geometry in white matter because of the potential to be more sensitive to small pores compared to conventional time-dependent diffusion. However, analytical expressions for the diffusion spectrum of particles have only been derived for simple, restricting geometries such as cylinders, which are often used as a model for intra-axonal diffusion. The extra-axonal space is more complex, but the diffusion spectrum has largely not been modeled. We propose a model for the extra-axonal space, which can be used for interpretation of experimental data. THEORY AND METHODS An empirical model describing the extra-axonal space diffusion spectrum was compared with simulated spectra. Spectra were simulated using Monte Carlo methods for idealized, regularly and randomly packed axons over a wide range of packing densities and spatial scales. The model parameters are related to the microstructural properties of tortuosity, axonal radius, and separation for regularly packed axons and pore size for randomly packed axons. RESULTS Forward model predictions closely matched simulations. The model fitted the simulated spectra well and accurately estimated microstructural properties. CONCLUSIONS This simple model provides expressions that relate the diffusion spectrum to biologically relevant microstructural properties.
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Affiliation(s)
- Wilfred W Lam
- Centre for Functional MRI of the Brain, University of Oxford, Oxford, UK
| | - Saâd Jbabdi
- Centre for Functional MRI of the Brain, University of Oxford, Oxford, UK
| | - Karla L Miller
- Centre for Functional MRI of the Brain, University of Oxford, Oxford, UK
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32
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Bai R, Koay CG, Hutchinson E, Basser PJ. A framework for accurate determination of the T₂ distribution from multiple echo magnitude MRI images. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2014; 244:53-63. [PMID: 24859198 PMCID: PMC4086921 DOI: 10.1016/j.jmr.2014.04.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Revised: 03/30/2014] [Accepted: 04/24/2014] [Indexed: 05/08/2023]
Abstract
Measurement of the T2 distribution in tissues provides biologically relevant information about normal and abnormal microstructure and organization. Typically, the T2 distribution is obtained by fitting the magnitude MR images acquired by a multi-echo MRI pulse sequence using an inverse Laplace transform (ILT) algorithm. It is well known that the ideal magnitude MR signal follows a Rician distribution. Unfortunately, studies attempting to establish the validity and efficacy of the ILT algorithm assume that these input signals are Gaussian distributed. Violation of the normality (or Gaussian) assumption introduces unexpected artifacts, including spurious cerebrospinal fluid (CSF)-like long T2 components; bias of the true geometric mean T2 values and in the relative fractions of various components; and blurring of nearby T2 peaks in the T2 distribution. Here we apply and extend our previously proposed magnitude signal transformation framework to map noisy Rician-distributed magnitude multi-echo MRI signals into Gaussian-distributed signals with high accuracy and precision. We then perform an ILT on the transformed data to obtain an accurate T2 distribution. Additionally, we demonstrate, by simulations and experiments, that this approach corrects the aforementioned artifacts in magnitude multi-echo MR images over a large range of signal-to-noise ratios.
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Affiliation(s)
- Ruiliang Bai
- Section on Tissue Biophysics and Biomimetics, PPITS, NICHD, National Institutes of Health, Bethesda, MD 20892, USA; Biophysics Program, Institute for Physical Science and Technology, University of Maryland, College Park, MD 20740, USA.
| | - Cheng Guan Koay
- Department of Medical Physics, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
| | - Elizabeth Hutchinson
- Section on Tissue Biophysics and Biomimetics, PPITS, NICHD, National Institutes of Health, Bethesda, MD 20892, USA
| | - Peter J Basser
- Section on Tissue Biophysics and Biomimetics, PPITS, NICHD, National Institutes of Health, Bethesda, MD 20892, USA
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Benjamini D, Elsner JJ, Zilberman M, Nevo U. Pore size distribution of bioresorbable films using a 3-D diffusion NMR method. Acta Biomater 2014; 10:2762-8. [PMID: 24534719 DOI: 10.1016/j.actbio.2014.02.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Revised: 01/21/2014] [Accepted: 02/05/2014] [Indexed: 11/29/2022]
Abstract
Pore size distribution (PSD) within porous biomaterials is an important microstructural feature for assessing their biocompatibility, longevity and drug release kinetics. Scanning electron microscopy (SEM) is the most common method used to obtain the PSD of soft biomaterials. The method is highly invasive and user dependent, since it requires fracturing of the sample and then considers only the small portion that the user had acquired in the image. In the current study we present a novel nuclear magnetic resonance (NMR) method as an alternative method for estimation of PSD in soft porous materials. This noninvasive 3-D diffusion NMR method considers the entire volume of the specimen and eliminates the user's need to choose a specific field of view. Moreover, NMR does not involve exposure to ionizing radiation and can potentially have preclinical and clinical uses. The method was applied on four porous 50/50 poly(dl-lactic-co-glycolic acid) bioresorbable films with different porosities, which were created using the freeze-drying of inverted emulsions technique. We show that the proposed NMR method is able to address the main limitations associated with SEM-based PSD estimations by being non-destructive, depicting the full volume of the specimens and not being dependent on the magnification factor. Upon comparison, both methods yielded a similar PSD in the smaller pore size range (1-25μm), while the NMR-based method provided additional information on the larger pores (25-50μm).
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Affiliation(s)
- Dan Benjamini
- Department of Biomedical Engineering, The Iby and Aladar Fleischman Faculty of Engineering, Tel-Aviv University, Tel-Aviv 69978, Israel
| | - Jonathan J Elsner
- Department of Biomedical Engineering, The Iby and Aladar Fleischman Faculty of Engineering, Tel-Aviv University, Tel-Aviv 69978, Israel
| | - Meital Zilberman
- Department of Biomedical Engineering, The Iby and Aladar Fleischman Faculty of Engineering, Tel-Aviv University, Tel-Aviv 69978, Israel
| | - Uri Nevo
- Department of Biomedical Engineering, The Iby and Aladar Fleischman Faculty of Engineering, Tel-Aviv University, Tel-Aviv 69978, Israel.
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Paus T, Pesaresi M, French L. White matter as a transport system. Neuroscience 2014; 276:117-25. [PMID: 24508743 DOI: 10.1016/j.neuroscience.2014.01.055] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Revised: 01/14/2014] [Accepted: 01/29/2014] [Indexed: 12/14/2022]
Abstract
There are two ways to picture white matter: as a grid of electrical wires or a network of roads. The first metaphor captures the classical function of an axon as conductor of action potentials (and information) from one brain region to another. The second one points to the important role of axons in a bi-directional transport of biological molecules and organelles between the cell body and synapse. Given the wide variety of such cargoes, a well-functioning axonal transport is critical for a number of processes, including neurotransmission, metabolism and viability of neurons. This selective review will emphasize the need for considering axonal transport when interpreting functional consequences of inter-individual variations in the structural properties of white matter. We start by describing the space occupied by white matter and techniques used in vivo for its characterization. We then provide examples of key features of maturation and aging of white matter, as well as some of the common abnormalities observed in neurodevelopmental and neurodegenerative disorders. Next, we review work that motivated our focus on axonal diameter, and explain the relationships between transport and cytoskeleton within the axon. We will conclude by describing molecular machinery of axonal transport and genes that may contribute to inter-individual variations in axonal diameter and axonal transport.
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Affiliation(s)
- T Paus
- Rotman Research Institute, University of Toronto, Toronto, Canada.
| | - M Pesaresi
- Rotman Research Institute, University of Toronto, Toronto, Canada
| | - L French
- Rotman Research Institute, University of Toronto, Toronto, Canada
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35
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Lawrenz M, Finsterbusch J. Mapping measures of microscopic diffusion anisotropy in human brain white matter in vivo with double-wave-vector diffusion-weighted imaging. Magn Reson Med 2014; 73:773-83. [DOI: 10.1002/mrm.25140] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Revised: 12/12/2013] [Accepted: 01/02/2014] [Indexed: 11/07/2022]
Affiliation(s)
- Marco Lawrenz
- Department of Systems Neuroscience; University Medical Center Hamburg-Eppendorf; Hamburg Germany
- Neuroimage Nord; University Medical Centers Hamburg-Kiel-Lübeck; Germany
| | - Jürgen Finsterbusch
- Department of Systems Neuroscience; University Medical Center Hamburg-Eppendorf; Hamburg Germany
- Neuroimage Nord; University Medical Centers Hamburg-Kiel-Lübeck; Germany
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